# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:48:43 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 6-chloro-4-(2-chlorophenyl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Cn2c3cc(Cl)cc(c4ccccc4Cl)c3nc2N5CCNCC5)cc(C)c1F
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 FV7  FV7  6-chloro-4-(2-chlorophenyl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole  ligand  58  33  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FV7
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 FV7  N1   N   N     0  -0.476   1.0987   1.3211  -0.5270
 FV7  N3   N   NH1   0  -0.601  -1.7529   5.2164  -1.6176
 FV7  C4   C   CH2   0  -0.450  -1.9658  -0.0260  -1.9002
 FV7  C5   C   CR5   0   0.683  -0.0677   1.4468  -1.0973
 FV7  C6   C   CR56  0   0.153   1.3745  -0.0192  -0.5661
 FV7  C7   C   CR6   0  -0.030   2.4863  -0.7137  -0.0921
 FV7  C8   C   CR16  0  -0.281   2.5291  -2.0863  -0.3091
 FV7  C10  C   CR16  0  -0.273   0.3587  -2.0766  -1.4263
 FV7  C13  C   CR16  0  -0.312   4.8756  -0.0415   0.0282
 FV7  C15  C   CR16  0  -0.273   5.7457   1.2802   1.8317
 FV7  C17  C   CR6   0  -0.115   3.4309   0.6591   1.7932
 FV7  C20  C   CH2   0  -0.300  -1.5259   4.7088  -0.2779
 FV7  C21  C   CH2   0  -0.296  -0.4096   3.6812  -0.3003
 FV7  C22  C   CR16  0  -0.340  -3.0309   0.2358   0.3576
 FV7  C25  C   CR6   0   0.498  -4.1342  -1.5729   1.4099
 FV7  C1   C   CR6   0  -0.071  -3.8876  -2.4246   0.3473
 FV7  C    C   CH3   0  -0.716  -4.3618  -3.8465   0.3625
 FV7  C23  C   CR6   0  -0.065  -3.7310  -0.2455   1.4564
 FV7  C3   C   CR6   0   0.157  -2.7449  -0.5778  -0.7347
 FV7  C2   C   CR16  0  -0.364  -3.1795  -1.8950  -0.7292
 FV7  N    N   NR5   0  -0.556  -0.5860   0.2537  -1.5434
 FV7  C11  C   CR56  0   0.364   0.3376  -0.7080  -1.2134
 FV7  C9   C   CR6   0  -0.055   1.4818  -2.7390  -0.9593
 FV7  CL   CL  CL    0  -0.136   1.5893  -4.4581  -1.1840
 FV7  C12  C   CR6   0   0.160   3.5981  -0.0200   0.5864
 FV7  C16  C   CR16  0  -0.195   4.4875   1.3079   2.4145
 FV7  C14  C   CR16  0  -0.231   5.9425   0.5992   0.6391
 FV7  N2   N   NT    0  -0.543  -0.7744   2.6130  -1.2214
 FV7  C19  C   CH2   0  -0.295  -2.1313   4.1488  -2.5231
 FV7  C18  C   CH2   0  -0.328  -1.0203   3.1197  -2.5731
 FV7  H1   H   HNH1  0   0.358  -2.4747   5.9242  -1.5996
 FV7  H3   H   HCH2  0   0.291  -1.9766  -0.7214  -2.7411
 FV7  H4   H   HCH2  0   0.298  -2.4245   0.8955  -2.2502
 FV7  H5   H   HCR6  0   0.271   3.3772  -2.6573   0.0454
 FV7  H6   H   HCR6  0   0.283  -0.4402  -2.6052  -1.9275
 FV7  H7   H   HCR6  0   0.262   5.0267  -0.5626  -0.9086
 FV7  H8   H   HCR6  0   0.269   6.5689   1.7883   2.3158
 FV7  H9   H   HCH2  0   0.241  -1.2354   5.5330   0.3762
 FV7  H10  H   HCH2  0   0.197  -2.4229   4.2417   0.1592
 FV7  H11  H   HCH2  0   0.222   0.5335   4.1581  -0.5958
 FV7  H12  H   HCH2  0   0.252  -0.2693   3.2617   0.6952
 FV7  H13  H   HCR6  0   0.248  -2.7132   1.2728   0.3524
 FV7  H14  H   HCH3  0   0.253  -3.5762   0.2409   3.5495
 FV7  H15  H   HCH3  0   0.246  -3.6879   1.6334   2.4795
 FV7  H16  H   HCH3  0   0.252  -5.1190   0.6707   2.8289
 FV7  H17  H   HCH3  0   0.252  -5.4499  -3.9081   0.4123
 FV7  H18  H   HCH3  0   0.249  -4.0410  -4.3645  -0.5394
 FV7  H19  H   HCH3  0   0.251  -3.9676  -4.3950   1.2189
 FV7  H20  H   HCR6  0   0.258  -2.9744  -2.5347  -1.5804
 FV7  H21  H   HCR6  0   0.280   4.3296   1.8259   3.3507
 FV7  H22  H   HCR6  0   0.264   6.9225   0.5687   0.1823
 FV7  H23  H   HCH2  0   0.201  -3.0644   3.6429  -2.2273
 FV7  H24  H   HCH2  0   0.242  -2.2831   4.5583  -3.5232
 FV7  H25  H   HCH2  0   0.241  -0.1070   3.5783  -2.9746
 FV7  H26  H   HCH2  0   0.259  -1.2957   2.3069  -3.2437
 FV7  CL1  CL  CL    0  -0.124   1.8879   0.6658   2.5800
 FV7  C24  C   CH3   0  -0.717  -4.0462   0.6182   2.6402
 FV7  F    F   F     0  -0.310  -4.8126  -2.0615   2.4665

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 FV7  C    C1   single    1.499  0.020  1.499
 FV7  N3   C20  single    1.450  0.020  1.450
 FV7  N3   C19  single    1.450  0.020  1.450
 FV7  F    C25  single    1.347  0.020  1.347
 FV7  C20  C21  single    1.517  0.020  1.517
 FV7  C1   C25  aromatic  1.384  0.020  1.384
 FV7  C1   C2   aromatic  1.393  0.020  1.393
 FV7  C19  C18  single    1.515  0.020  1.515
 FV7  C25  C23  aromatic  1.388  0.020  1.388
 FV7  C2   C3   aromatic  1.387  0.020  1.387
 FV7  C21  N2   single    1.457  0.020  1.457
 FV7  C23  C24  single    1.499  0.020  1.499
 FV7  C23  C22  aromatic  1.389  0.020  1.389
 FV7  C18  N2   single    1.464  0.020  1.464
 FV7  N2   C5   single    1.369  0.020  1.369
 FV7  C3   C22  aromatic  1.392  0.020  1.392
 FV7  C3   C4   single    1.507  0.020  1.507
 FV7  C4   N    single    1.452  0.020  1.452
 FV7  C5   N    aromatic  1.375  0.020  1.375
 FV7  C5   N1   aromatic  1.304  0.020  1.304
 FV7  N    C11  aromatic  1.374  0.020  1.374
 FV7  N1   C6   aromatic  1.369  0.020  1.369
 FV7  CL1  C17  single    1.732  0.020  1.732
 FV7  C11  C6   aromatic  1.403  0.020  1.403
 FV7  C11  C10  aromatic  1.385  0.020  1.385
 FV7  C6   C7   aromatic  1.394  0.020  1.394
 FV7  C17  C16  aromatic  1.387  0.020  1.387
 FV7  C17  C12  aromatic  1.395  0.020  1.395
 FV7  C16  C15  aromatic  1.387  0.020  1.387
 FV7  C10  C9   aromatic  1.385  0.020  1.385
 FV7  C7   C12  single    1.476  0.020  1.476
 FV7  C7   C8   aromatic  1.390  0.020  1.390
 FV7  C12  C13  aromatic  1.394  0.020  1.394
 FV7  C15  C14  aromatic  1.387  0.020  1.387
 FV7  C9   C8   aromatic  1.395  0.020  1.395
 FV7  C9   CL   single    1.737  0.020  1.737
 FV7  C13  C14  aromatic  1.386  0.020  1.386
 FV7  N3   H1   single    0.890  0.020  1.040
 FV7  C4   H3   single    0.970  0.020  1.090
 FV7  C4   H4   single    0.970  0.020  1.090
 FV7  C8   H5   single    0.930  0.020  1.080
 FV7  C10  H6   single    0.930  0.020  1.080
 FV7  C13  H7   single    0.930  0.020  1.080
 FV7  C15  H8   single    0.930  0.020  1.080
 FV7  C20  H9   single    0.970  0.020  1.090
 FV7  C20  H10  single    0.970  0.020  1.090
 FV7  C21  H11  single    0.970  0.020  1.090
 FV7  C21  H12  single    0.970  0.020  1.090
 FV7  C22  H13  single    0.930  0.020  1.080
 FV7  C24  H14  single    0.970  0.020  1.090
 FV7  C24  H15  single    0.970  0.020  1.090
 FV7  C24  H16  single    0.970  0.020  1.090
 FV7  C    H17  single    0.970  0.020  1.090
 FV7  C    H18  single    0.970  0.020  1.090
 FV7  C    H19  single    0.970  0.020  1.090
 FV7  C2   H20  single    0.930  0.020  1.080
 FV7  C16  H21  single    0.930  0.020  1.080
 FV7  C14  H22  single    0.930  0.020  1.080
 FV7  C19  H23  single    0.970  0.020  1.090
 FV7  C19  H24  single    0.970  0.020  1.090
 FV7  C18  H25  single    0.970  0.020  1.090
 FV7  C18  H26  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 FV7  C6   N1   C5   105.19  3.000
 FV7  H1   N3   C19  109.89  3.000
 FV7  H1   N3   C20  109.89  3.000
 FV7  C19  N3   C20  111.10  3.000
 FV7  H4   C4   H3   106.73  3.000
 FV7  H4   C4   N    108.46  3.000
 FV7  H3   C4   N    108.75  3.000
 FV7  H4   C4   C3   109.95  3.000
 FV7  H3   C4   C3   110.95  3.000
 FV7  N    C4   C3   111.83  3.000
 FV7  N2   C5   N    121.00  3.000
 FV7  N    C5   N1   113.28  3.000
 FV7  N2   C5   N1   125.68  3.000
 FV7  C11  C6   C7   120.12  3.000
 FV7  C7   C6   N1   129.70  3.000
 FV7  C11  C6   N1   110.18  3.000
 FV7  C12  C7   C8   120.84  3.000
 FV7  C8   C7   C6   117.60  3.000
 FV7  C12  C7   C6   121.54  3.000
 FV7  H5   C8   C9   119.62  3.000
 FV7  H5   C8   C7   119.60  3.000
 FV7  C9   C8   C7   120.77  3.000
 FV7  H6   C10  C9   121.45  3.000
 FV7  H6   C10  C11  122.90  3.000
 FV7  C9   C10  C11  115.65  3.000
 FV7  H7   C13  C14  119.76  3.000
 FV7  H7   C13  C12  118.79  3.000
 FV7  C14  C13  C12  121.44  3.000
 FV7  H8   C15  C14  120.49  3.000
 FV7  H8   C15  C16  119.53  3.000
 FV7  C14  C15  C16  119.98  3.000
 FV7  C16  C17  CL1  118.26  3.000
 FV7  C16  C17  C12  121.60  3.000
 FV7  CL1  C17  C12  120.11  3.000
 FV7  H10  C20  H9   107.40  3.000
 FV7  H10  C20  C21  108.52  3.000
 FV7  H9   C20  C21  108.93  3.000
 FV7  H10  C20  N3   112.79  3.000
 FV7  H9   C20  N3   109.33  3.000
 FV7  C21  C20  N3   109.78  3.000
 FV7  H12  C21  H11  107.63  3.000
 FV7  H12  C21  N2   109.12  3.000
 FV7  H11  C21  N2   111.32  3.000
 FV7  H12  C21  C20  110.00  3.000
 FV7  H11  C21  C20  110.00  3.000
 FV7  N2   C21  C20  108.76  3.000
 FV7  H13  C22  C3   119.67  3.000
 FV7  H13  C22  C23  118.86  3.000
 FV7  C3   C22  C23  121.46  3.000
 FV7  C23  C25  C1   124.23  3.000
 FV7  C23  C25  F    117.82  3.000
 FV7  C1   C25  F    117.94  3.000
 FV7  C2   C1   C    121.96  3.000
 FV7  C2   C1   C25  116.74  3.000
 FV7  C    C1   C25  121.31  3.000
 FV7  H19  C    H18  107.74  3.000
 FV7  H19  C    H17  107.23  3.000
 FV7  H18  C    H17  107.75  3.000
 FV7  H19  C    C1   111.76  3.000
 FV7  H18  C    C1   110.47  3.000
 FV7  H17  C    C1   111.69  3.000
 FV7  C25  C23  C24  121.09  3.000
 FV7  C24  C23  C22  122.09  3.000
 FV7  C25  C23  C22  116.82  3.000
 FV7  C2   C3   C22  119.19  3.000
 FV7  C22  C3   C4   119.96  3.000
 FV7  C2   C3   C4   120.86  3.000
 FV7  H20  C2   C3   119.86  3.000
 FV7  H20  C2   C1   118.58  3.000
 FV7  C3   C2   C1   121.56  3.000
 FV7  C11  N    C5   106.03  3.000
 FV7  C11  N    C4   124.26  3.000
 FV7  C5   N    C4   127.22  3.000
 FV7  N    C11  C10  131.68  3.000
 FV7  C10  C11  C6   123.01  3.000
 FV7  N    C11  C6   105.31  3.000
 FV7  CL   C9   C10  118.67  3.000
 FV7  CL   C9   C8   118.48  3.000
 FV7  C10  C9   C8   122.84  3.000
 FV7  C17  C12  C13  117.63  3.000
 FV7  C13  C12  C7   119.94  3.000
 FV7  C17  C12  C7   122.43  3.000
 FV7  H21  C16  C17  120.04  3.000
 FV7  H21  C16  C15  120.38  3.000
 FV7  C17  C16  C15  119.58  3.000
 FV7  H22  C14  C15  120.36  3.000
 FV7  H22  C14  C13  119.88  3.000
 FV7  C15  C14  C13  119.77  3.000
 FV7  C18  N2   C21  111.83  3.000
 FV7  C18  N2   C5   117.71  3.000
 FV7  C21  N2   C5   115.97  3.000
 FV7  H24  C19  H23  107.49  3.000
 FV7  H24  C19  C18  109.07  3.000
 FV7  H23  C19  C18  108.54  3.000
 FV7  H24  C19  N3   109.40  3.000
 FV7  H23  C19  N3   113.04  3.000
 FV7  C18  C19  N3   109.22  3.000
 FV7  H26  C18  H25  107.27  3.000
 FV7  H26  C18  C19  109.98  3.000
 FV7  H25  C18  C19  109.78  3.000
 FV7  H26  C18  N2   110.64  3.000
 FV7  H25  C18  N2   110.02  3.000
 FV7  C19  C18  N2   109.13  3.000
 FV7  H16  C24  H15  107.73  3.000
 FV7  H16  C24  H14  107.23  3.000
 FV7  H15  C24  H14  107.69  3.000
 FV7  H16  C24  C23  111.80  3.000
 FV7  H15  C24  C23  110.58  3.000
 FV7  H14  C24  C23  111.61  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 FV7  CONST_01  C11  N    C5   N1      0.00   0.0  0
 FV7  CONST_02  N    C11  C6   N1      0.00   0.0  0
 FV7  CONST_03  C10  C11  C6   N1    180.00   0.0  0
 FV7  CONST_04  C12  C7   C6   N1      0.00   0.0  0
 FV7  CONST_05  C8   C7   C6   N1    180.00   0.0  0
 FV7  CONST_06  C6   C11  N    C5      0.00   0.0  0
 FV7  CONST_07  C10  C11  N    C5    180.00   0.0  0
 FV7  CONST_08  C11  C6   N1   C5      0.00   0.0  0
 FV7  CONST_09  C7   C6   N1   C5    180.00   0.0  0
 FV7  CONST_10  N    C5   N1   C6      0.00   0.0  0
 FV7  CONST_11  C9   C10  C11  C6      0.00   0.0  0
 FV7  CONST_14  C9   C8   C7   C6      0.00   0.0  0
 FV7  CONST_15  N    C11  C6   C7    180.00   0.0  0
 FV7  CONST_16  C10  C11  C6   C7      0.00   0.0  0
 FV7  CONST_17  C16  C17  C12  C7    180.00   0.0  0
 FV7  CONST_18  C14  C13  C12  C7    180.00   0.0  0
 FV7  CONST_19  C10  C9   C8   C7      0.00   0.0  0
 FV7  CONST_20  C11  C6   C7   C8      0.00   0.0  0
 FV7  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 FV7  CONST_24  C16  C17  C12  C13     0.00   0.0  0
 FV7  CONST_25  C16  C15  C14  C13     0.00   0.0  0
 FV7  CONST_26  C12  C17  C16  C15     0.00   0.0  0
 FV7  CONST_27  C12  C13  C14  C15     0.00   0.0  0
 FV7  CONST_28  C14  C15  C16  C17     0.00   0.0  0
 FV7  CONST_29  C14  C13  C12  C17     0.00   0.0  0
 FV7  CONST_30  C1   C25  C23  C22     0.00   0.0  0
 FV7  CONST_31  C1   C2   C3   C22     0.00   0.0  0
 FV7  CONST_32  C3   C2   C1   C25     0.00   0.0  0
 FV7  CONST_33  C3   C22  C23  C25     0.00   0.0  0
 FV7  CONST_34  C2   C1   C25  C23     0.00   0.0  0
 FV7  CONST_35  C2   C3   C22  C23     0.00   0.0  0
 FV7  CONST_36  C9   C10  C11  N     180.00   0.0  0
 FV7  CONST_37  C12  C7   C6   C11   180.00   0.0  0
 FV7  CONST_38  C12  C7   C8   C9    180.00   0.0  0
 FV7  CONST_39  N2   C5   N1   C6    180.00   0.0  0
 FV7  CONST_40  N2   C5   N    C11   180.00   0.0  0
 FV7  CONST_42  C1   C2   C3   C4    180.00   0.0  0
 FV7  CONST_43  C23  C22  C3   C4    180.00   0.0  0
 FV7  CONST_44  N2   C5   N    C4      0.00   0.0  0
 FV7  CONST_47  CL1  C17  C12  C7      0.00   0.0  0
 FV7  CONST_48  CL   C9   C8   C7    180.00   0.0  0
 FV7  CONST_49  CL1  C17  C12  C13   180.00   0.0  0
 FV7  CONST_50  CL1  C17  C16  C15   180.00   0.0  0
 FV7  CONST_51  F    C25  C23  C22   180.00   0.0  0
 FV7  CONST_52  C1   C25  C23  C24   180.00   0.0  0
 FV7  CONST_53  C3   C22  C23  C24   180.00   0.0  0
 FV7  CONST_54  C2   C1   C25  F     180.00   0.0  0
 FV7  CONST_55  C23  C25  C1   C     180.00   0.0  0
 FV7  CONST_56  C3   C2   C1   C     180.00   0.0  0
 FV7  CONST_57  CL   C9   C10  C11   180.00   0.0  0
 FV7  CONST_58  H6   C10  C11  C6    180.00   0.0  0
 FV7  CONST_59  H5   C8   C7   C6    180.00   0.0  0
 FV7  CONST_60  H7   C13  C12  C7      0.00   0.0  0
 FV7  CONST_61  H8   C15  C14  C13   180.00   0.0  0
 FV7  CONST_62  H20  C2   C3   C22   180.00   0.0  0
 FV7  CONST_63  H13  C22  C23  C25   180.00   0.0  0
 FV7  CONST_64  H21  C16  C17  C12   180.00   0.0  0
 FV7  CONST_65  H22  C14  C13  C12   180.00   0.0  0
 FV7  Var_01    C21  N2   C5   N1    -20.26  30.0  2
 FV7  Var_02    N2   C21  C20  N3    -57.75  30.0  1
 FV7  Var_03    N2   C18  C19  N3     57.95  30.0  1
 FV7  Var_04    C20  C21  N2   C5   -163.05  30.0  1
 FV7  Var_05    C19  C18  N2   C5    163.39  30.0  1
 FV7  Var_06    C18  C19  N3   C20   -60.00  30.0  1
 FV7  Var_07    C19  N3   C20  C21    60.10  30.0  1
 FV7  Var_08    C3   C4   N    C5    -92.85  30.0  1
 FV7  Var_09    N    C4   C3   C22    68.42  30.0  2
 FV7  Var_10    H14  C24  C23  C22  -117.73  30.0  2
 FV7  Var_11    H17  C    C1   C25    62.23  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 FV7  plan-1  C7   0.020
 FV7  plan-1  C13  0.020
 FV7  plan-1  C15  0.020
 FV7  plan-1  C17  0.020
 FV7  plan-1  C12  0.020
 FV7  plan-1  C16  0.020
 FV7  plan-1  C14  0.020
 FV7  plan-1  H7   0.020
 FV7  plan-1  H8   0.020
 FV7  plan-1  H21  0.020
 FV7  plan-1  H22  0.020
 FV7  plan-1  CL1  0.020
 FV7  plan-2  C4   0.020
 FV7  plan-2  C22  0.020
 FV7  plan-2  C25  0.020
 FV7  plan-2  C1   0.020
 FV7  plan-2  C    0.020
 FV7  plan-2  C23  0.020
 FV7  plan-2  C3   0.020
 FV7  plan-2  C2   0.020
 FV7  plan-2  H13  0.020
 FV7  plan-2  H20  0.020
 FV7  plan-2  C24  0.020
 FV7  plan-2  F    0.020
 FV7  plan-3  N1   0.020
 FV7  plan-3  C4   0.020
 FV7  plan-3  C5   0.020
 FV7  plan-3  C6   0.020
 FV7  plan-3  C7   0.020
 FV7  plan-3  C8   0.020
 FV7  plan-3  C10  0.020
 FV7  plan-3  N    0.020
 FV7  plan-3  C11  0.020
 FV7  plan-3  C9   0.020
 FV7  plan-3  CL   0.020
 FV7  plan-3  C12  0.020
 FV7  plan-3  N2   0.020
 FV7  plan-3  H5   0.020
 FV7  plan-3  H6   0.020

